test_workflows/assert_h5mu_slots
Description
Test helper. Reads a modality from an output h5mu and asserts that the expected
.obs columns, .obsm keys, .obsp keys and .uns keys are all present, and that any
slots listed as absent are not present. Raises an error listing any missing slots
(expected but absent) or unexpected slots (listed as absent but present).
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Output h5mu file to validate. |
--modality | string | Modality to inspect. |
Expected slots
Name | Type & Properties | Description |
|---|---|---|
--obs | string multiple | Expected .obs column names. |
--obsm | string multiple | Expected .obsm keys. |
--obsp | string multiple | Expected .obsp keys. |
--uns | string multiple | Expected .uns keys. |
Unexpected slots
Name | Type & Properties | Description |
|---|---|---|
--obs_absent | string multiple | .obs column names that must not be present. |
--obsm_absent | string multiple | .obsm keys that must not be present. |
--obsp_absent | string multiple | .obsp keys that must not be present. |
--uns_absent | string multiple | .uns keys that must not be present. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
modality: [ "rna" ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline_composed.git \
-revision v0.3.0 \
-main-script target/nextflow/test_workflows/assert_h5mu_slots/main.nf \
-params-file params.yaml Relationships
Used by
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No components use this component.
Current component
test_workflows/assert_h5mu_slotsopenpipeline_composed v0.3.0
Uses
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No component dependencies found.